geek culture By Gregori Pujol March 24, 2020 at 9:05 am
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The availability of Parabricks, the GPU-optimized bioinformatics software suite dedicated to genomic analysis, will help accelerate research on the understanding of the new coronavirus and the fight against Covid-19.

A real race against the clock is underway and mobilizes players from around the world. In particular, those of health and research. In response to the pandemic, NVIDIA has decided to share with researchers working on it, software tools capable of speeding up the discovery process in order to better understand the coronavirus and provide faster responses.

For the past few days, NVIDIA has been providing a free 90-day Parabricks license for any researcher involved in the fight against the coronavirus. Covering the entire GATK (Genome Analysis Toolkit) pipeline, which is the industry standard for identifying SNP (Single-nucleotide Polymorphysm) and DNA comparisons, Parabricks is taking advantage of GPU acceleration to reduce lead times. genomic analysis up to 50 times.

All researchers with access to NVIDIA GPUs can complete this form to request a free Parabricks license. For researchers working on Oxford Nanopore long read sequence data, a set of GPU-optimized software tools is available on GitHub. In addition, the following applications immediately integrate NVIDIA GPU accelerations: Medaka, Racon, Raven, Reticulatus, Unicycler.

Researchers are sequencing the coronavirus and genomes of people with Covid-19 to better understand, among other things, the spread of the disease, and to identify the populations most at risk; but genomic analysis takes time and requires computing power.

Parabricks software, whose team joined NVIDIA in December 2019, is able to reduce the time required to call variants on human whole genome sequences (WGS), reducing it from a few days to less than one time, using only one server. Given the unprecedented spread of the pandemic, achieving results in hours rather than days can have a very significant impact on the understanding of the virus, its evolution and, therefore, on vaccine development.

NVIDIA is also mobilizing its ecosystem of partners in this urgent effort to help the research community. Discussions are currently underway with cloud service providers and centers with supercomputers in order to provide additional computing resources and offer free access to Parabricks solutions on their platforms.
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